How to use
To use the code you will need
1) *.3d distributions calculated with RISM-MOL-3D
2) *.grd grid files for these distributions'
3) solvent.xyz (solvent.pdb) - file in xyz or pdb format with solvent coordinates
4) distributions.txt - file wich defines, which atom in solvent.xyz corresponds to which *.3d distribution
5) solute.xyz (solute.pdb) - file in xyz or pdb format with solute coordinated
EXAMPLE:
With the code is provided example: cyclodextrine in water distributions
Files: CD_in_water_g0.3d - water oxygen distribution around the alpha-cyclodextrine
CD_in_water_g1.3d - water hydrogen distribution around the alpha-cyclodextrine
CD_in_water_X.grd, CD_in_water_Y.grd, CD_in_water_Z.grd - grid files for distributions
CD.xyz - coordinates of cyclodextrine
water.xyz - coordinates of water
distributions.txt - file which contain three lines:
CD_in_water_g0.3d
CD_in_water_g1.3d
CD_in_water_g1.3d
This means, that in water.xyz file the first atom (oxygen) corresponds to the CD_in_water_g0.3d distibution, and two other atoms (hydrogens) correspond to the CD_in_water_g1.3d distribution
STEP1: we need to calculate the most probable rotations of the molecules at each point
To do this:
./getBestRotationsFast water.xyz distributions.txt CD_in_water CD_in_water 2
Here water.xyz is a solvent file
distributions.txt is a distribution correspondance file
CD_in_water (first) is the grid prefix (by convention the grid files are prefix_X.grd, prefix_Y.grd, prefix_Z.grd)
CD_in_water (second) is the output files prefix
2 is the threshold. The point where all the input distributions are less then the threshold are not considered.
Four files will be created:
CD_in_water_Gmax.3d - maximal water relative density at each point
CD_in_water_PhiMax.3d, CD_in_water_PsiMax.3d, CD_in_water_ThetaMax.3d - euler angles at each point which give the maximal water density
STEP2: convert the Gmax and Euler angles to the binding molecules in xyz format.
To do this:
./createBindingMoleculesXYZ water.xyz CD_in_water CD_in_water 2 > binding.xyz
Here water.xyz is a solvent file
CD_in_water (first) is a grid prefix
CD_in_water (second) is a prefix for Gmax and Euler angle files
2 is the threshold. The points where Gmax is less than threshold will not be visualized
binding.xyz is the output xyz
STEP3: convert Gmax to the dx format (readable by vmd)
To do this:
./3DtoDX CD_in_water CD_in_water_Gmax.3d CD_in_water_Gmax.dx
Here CD_in_water is the grid prefix
CD_in_water_Gmax.3d is the input *.3d file
CD_in_water_Gmax.dx is the output *.dx file
STEP4: visualization
Run vmd
1) Open the molecule CD.xyz ( MainMenu-> New Molecule, in the field "filename" type CD.xyz, press load, close the window )
2) load the 3D distribution ( Main manu, right click on CD.xyz, select "Load Data into Molecule", at the new window type "CD_in_water_Gmax.dx" in the field "Filename", press load, close the window)
3) load the binding molecules ( MainMenu-> New Molecule, in the field "filename" type binding.xyz, press load, close the window )
Now, you have everything in VMD.
To visualize Gmax, go to "Main Menu -> Graphics->representations and create new representation "Isosurface" for CD.xyz )
To make the picture looking good i used the following parameters for the visualizing:
binding.xyz - VDW, sphere size 0.6
CD.xyz - surf, silver color
isosurface ( new representation for CD.xyz) - isovalue 2.5, solid color, blue
Program for visualizing the most probable positions of binding molecules
Download:
How to Install:
0) download
1) Unpack
tar -xzf rism-vmol_2012_05_31.tar.gz
2) go to the created folder
cd rism-vmol_2012_05_31
3) compile FFTW library
./makeFFTW
4) compile the source code
./makeAll
5) (optionally) setup paths
export PATH=$PATH:$(pwd)
echo export 'PATH=$PATH:'$(pwd) >> ~/.bashrc
How to use
To use the code you will need
1) *.3d distributions calculated with RISM-MOL-3D
2) *.grd grid files for these distributions'
3) solvent.xyz (solvent.pdb) - file in xyz or pdb format with solvent coordinates
4) distributions.txt - file wich defines, which atom in solvent.xyz corresponds to which *.3d distribution
5) solute.xyz (solute.pdb) - file in xyz or pdb format with solute coordinated
EXAMPLE:
With the code is provided example: cyclodextrine in water distributions
Files: CD_in_water_g0.3d - water oxygen distribution around the alpha-cyclodextrine
CD_in_water_g1.3d - water hydrogen distribution around the alpha-cyclodextrine
CD_in_water_X.grd, CD_in_water_Y.grd, CD_in_water_Z.grd - grid files for distributions
CD.xyz - coordinates of cyclodextrine
water.xyz - coordinates of water
distributions.txt - file which contain three lines:
CD_in_water_g0.3d
CD_in_water_g1.3d
CD_in_water_g1.3d
This means, that in water.xyz file the first atom (oxygen) corresponds to the CD_in_water_g0.3d distibution, and two other atoms (hydrogens) correspond to the CD_in_water_g1.3d distribution
STEP1: we need to calculate the most probable rotations of the molecules at each point
To do this:
./getBestRotationsFast water.xyz distributions.txt CD_in_water CD_in_water 2
Here water.xyz is a solvent file
distributions.txt is a distribution correspondance file
CD_in_water (first) is the grid prefix (by convention the grid files are prefix_X.grd, prefix_Y.grd, prefix_Z.grd)
CD_in_water (second) is the output files prefix
2 is the threshold. The point where all the input distributions are less then the threshold are not considered.
Four files will be created:
CD_in_water_Gmax.3d - maximal water relative density at each point
CD_in_water_PhiMax.3d, CD_in_water_PsiMax.3d, CD_in_water_ThetaMax.3d - euler angles at each point which give the maximal water density
STEP2: convert the Gmax and Euler angles to the binding molecules in xyz format.
To do this:
./createBindingMoleculesXYZ water.xyz CD_in_water CD_in_water 2 > binding.xyz
Here water.xyz is a solvent file
CD_in_water (first) is a grid prefix
CD_in_water (second) is a prefix for Gmax and Euler angle files
2 is the threshold. The points where Gmax is less than threshold will not be visualized
binding.xyz is the output xyz
STEP3: convert Gmax to the dx format (readable by vmd)
To do this:
./3DtoDX CD_in_water CD_in_water_Gmax.3d CD_in_water_Gmax.dx
Here CD_in_water is the grid prefix
CD_in_water_Gmax.3d is the input *.3d file
CD_in_water_Gmax.dx is the output *.dx file
STEP4: visualization
Run vmd
1) Open the molecule CD.xyz ( MainMenu-> New Molecule, in the field "filename" type CD.xyz, press load, close the window )
2) load the 3D distribution ( Main manu, right click on CD.xyz, select "Load Data into Molecule", at the new window type "CD_in_water_Gmax.dx" in the field "Filename", press load, close the window)
3) load the binding molecules ( MainMenu-> New Molecule, in the field "filename" type binding.xyz, press load, close the window )
Now, you have everything in VMD.
To visualize Gmax, go to "Main Menu -> Graphics->representations and create new representation "Isosurface" for CD.xyz )
To make the picture looking good i used the following parameters for the visualizing:
binding.xyz - VDW, sphere size 0.6
CD.xyz - surf, silver color
isosurface ( new representation for CD.xyz) - isovalue 2.5, solid color, blue
the result is below: